The Second Classroom, as an important complement and extension of the First Classroom teaching, plays a very active part in improving comprehensive abilities for the students. Especially for engineering students in applied universities, in recent years, the Second Classroom has gradually been regarded as the main platform for cultivating innovative quality and practical ability of the students. Teachers, which are main body of teaching, play a key guiding role in the Second Classroom teaching. It is meaningful to study teaching methods in the Second Classroom for engineering majors of applied universities, yet there are few studies in this area. In this paper, we mainly studied the teaching methods of the Second Classroom for engineering in applied university. Different types of courses in the Second Classroom, which is considered to be classified into practice-based and theory-based course by us, put forward different teaching methods. We respectively take one course as an example to analyze the main teaching methods for each of them. Then we proposed to design microlecture for relevant courses to conduct the Second Classroom instruction. Because of links between the two sample courses, we combined them as one microlecture to instruct students learning in the Second Classroom teaching. Through the questionnaire survey, the microlecture teaching method we have designed can effectively guide the activities of the Second classroom and it was welcomed by the students.